org.jmol.adapter.readers.quantum
Class SpartanInputReader

java.lang.Object
  org.jmol.adapter.smarter.AtomSetCollectionReader
      org.jmol.adapter.readers.quantum.BasisFunctionReader
          org.jmol.adapter.readers.quantum.SpartanInputReader

Direct Known Subclasses:

OdysseyReader, SpartanSmolReader

public abstract class SpartanInputReader
extends BasisFunctionReader

Field Summary

protected int	atomCount
protected String	bondData
(package private) String	constraints
protected int	modelAtomCount
protected String	modelName

Fields inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader

alphaBeta, CANONICAL_DC_LIST, CANONICAL_DS_LIST, CANONICAL_FC_LIST, CANONICAL_FS_LIST, dfCoefMaps, ignoreMOs, moData, nOrbitals, orbitals, shells

Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doc, doCheckUnitCell, doPackUnitCell, doProcessLines, filter, filterHetero, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, reader, readerName, readMolecularOrbitals, spaceGroup, stateScriptVersionInt, supercell, symmetry, templateAtomCount, useAltNames, vibrationNumber, viewer

Constructor Summary

SpartanInputReader()

Method Summary

private void	readAtomNames()
private void	readBonds(int atomCount0)
private void	readConstraints()
private void	readInputAtoms()
private void	readInputHeader()
protected void	readInputRecords()
private void	readTransform()

Methods inherited from class org.jmol.adapter.readers.quantum.BasisFunctionReader

canonicalizeQuantumSubshellTag, filterMO, fixSlaterTypes, getDfCoefMaps, getDFMap, isQuantumBasisSupported, setMO

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLine, checkLineForScript, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlock, fillFloatArray, fillFrequencyData, filterAtom, finalizeReader, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokens, getTokens, getTokensFloat, initializeReader, initializeSymmetry, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseStringInfestedFloatArray, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, processBinaryDocument, processXml, read3Vectors, readData, readLine, readLines, set2D, setAtomCoord, setAtomCoord, setFilter, setFractionalCoordinates, setIsPDB, setMOData, setPdb, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

modelName

protected String modelName

modelAtomCount

protected int modelAtomCount

atomCount

protected int atomCount

bondData

protected String bondData

constraints

String constraints

Constructor Detail

SpartanInputReader

public SpartanInputReader()

Method Detail

readInputRecords

protected void readInputRecords()
                         throws Exception

Throws:

Exception

readConstraints

private void readConstraints()
                      throws Exception

Throws:

Exception

readTransform

private void readTransform()
                    throws Exception

Throws:

Exception

readInputHeader

private void readInputHeader()
                      throws Exception

Throws:

Exception

readInputAtoms

private void readInputAtoms()
                     throws Exception

Throws:

Exception

readAtomNames

private void readAtomNames()
                    throws Exception

Throws:

Exception

readBonds

private void readBonds(int atomCount0)
                throws Exception

Throws:

Exception